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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:COPB2-NMD3 (FusionGDB2 ID:HG9276TG51068)

Fusion Gene Summary for COPB2-NMD3

check button Fusion gene summary
Fusion gene informationFusion gene name: COPB2-NMD3
Fusion gene ID: hg9276tg51068
HgeneTgene
Gene symbol

COPB2

NMD3

Gene ID

9276

51068

Gene nameCOPI coat complex subunit beta 2NMD3 ribosome export adaptor
SynonymsMCPH19|beta'-COPCGI-07
Cytomap('COPB2')('NMD3')

3q23

3q26.1

Type of geneprotein-codingprotein-coding
Descriptioncoatomer subunit beta'beta'-coat proteinbetaprime-COPcoatomer binding complex, beta prime subunitcoatomer protein complex subunit beta 2coatomer protein complex subunit beta primecoatomer protein complex, subunit beta 2 (beta prime)p10260S ribosomal export protein NMD3NMD3 homologhNMD3
Modification date2020031320200313
UniProtAcc

P35606

.
Ensembl transtripts involved in fusion geneENST00000333188, ENST00000510491, 
ENST00000507777, 
Fusion gene scores* DoF score8 X 8 X 4=2564 X 4 X 4=64
# samples 94
** MAII scorelog2(9/256*10)=-1.50814690367033
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COPB2 [Title/Abstract] AND NMD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOPB2(139108389)-NMD3(160955900), # samples:1
Anticipated loss of major functional domain due to fusion event.COPB2-NMD3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
COPB2-NMD3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCOPB2

GO:0006891

intra-Golgi vesicle-mediated transport

8335000



check button Fusion gene information
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4ESCATCGA-L5-A43HCOPB2chr3

139108389

-NMD3chr3

160955900

+


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Fusion Gene ORF analysis for COPB2-NMD3

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-intronENST00000333188ENST00000478160COPB2chr3

139108389

-NMD3chr3

160955900

+
5UTR-3CDSENST00000510491ENST00000351193COPB2chr3

139108389

-NMD3chr3

160955900

+
5UTR-3CDSENST00000510491ENST00000460469COPB2chr3

139108389

-NMD3chr3

160955900

+
5UTR-3CDSENST00000510491ENST00000472947COPB2chr3

139108389

-NMD3chr3

160955900

+
5UTR-intronENST00000510491ENST00000478160COPB2chr3

139108389

-NMD3chr3

160955900

+
Frame-shiftENST00000333188ENST00000351193COPB2chr3

139108389

-NMD3chr3

160955900

+
Frame-shiftENST00000333188ENST00000460469COPB2chr3

139108389

-NMD3chr3

160955900

+
Frame-shiftENST00000333188ENST00000472947COPB2chr3

139108389

-NMD3chr3

160955900

+
intron-3CDSENST00000507777ENST00000351193COPB2chr3

139108389

-NMD3chr3

160955900

+
intron-3CDSENST00000507777ENST00000460469COPB2chr3

139108389

-NMD3chr3

160955900

+
intron-3CDSENST00000507777ENST00000472947COPB2chr3

139108389

-NMD3chr3

160955900

+
intron-intronENST00000507777ENST00000478160COPB2chr3

139108389

-NMD3chr3

160955900

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for COPB2-NMD3


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
COPB2chr3139108389-NMD3chr3160955900+2.81E-070.99999976
COPB2chr3139108389-NMD3chr3160955900+2.81E-070.99999976


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for COPB2-NMD3


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:139108389/:160955900)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COPB2

P35606

.
FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity). {ECO:0000250}.; FUNCTION: This coatomer complex protein, essential for Golgi budding and vesicular trafficking, is a selective binding protein (RACK) for protein kinase C, epsilon type. It binds to Golgi membranes in a GTP-dependent manner (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for COPB2-NMD3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for COPB2-NMD3


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for COPB2-NMD3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for COPB2-NMD3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOPB2C3711387Autosomal Recessive Primary Microcephaly1ORPHANET
HgeneCOPB2C4540488MICROCEPHALY 19, PRIMARY, AUTOSOMAL RECESSIVE1UNIPROT